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Yorodumi- PDB-5zhl: Crystal structure of TrmD from Mycobacterium tuberculosis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zhl | ||||||
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Title | Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA methyltransferase | ||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis CDC 1551 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.W. / Nah, Q. / Liu, C.F. / Lescar, J. / Dedon, P.C. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. ...Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. / Liu, C.F. / Lescar, J. / Dedon, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zhl.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zhl.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zhl_validation.pdf.gz | 630.7 KB | Display | wwPDB validaton report |
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Full document | 5zhl_full_validation.pdf.gz | 631.3 KB | Display | |
Data in XML | 5zhl_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5zhl_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/5zhl ftp://data.pdbj.org/pub/pdb/validation_reports/zh/5zhl | HTTPS FTP |
-Related structure data
Related structure data | 5zhiC 5zhjC 5zhkC 5zhmC 5zhnC 6joeC 6jofC 5wyqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26170.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis CDC 1551 (bacteria) Strain: CDC 1551 / Gene: trmD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P9WFY6, UniProt: P9WFY7*PLUS, tRNA (guanine37-N1)-methyltransferase |
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#2: Chemical | ChemComp-9D0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM Bis-Tris at pH 6.5, 20%(w/v) PEG3350, 0.1M ammonium acetate; the crystal was soaked with 1 mM inhibitor. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→41.5 Å / Num. obs: 9936 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.25→2.37 Å / Rmerge(I) obs: 0.238 / Num. unique obs: 4380 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WYQ Resolution: 2.25→41.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.205
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Displacement parameters | Biso mean: 30.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→41.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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